From 5848b7b74dc706f12b4b48706d2ba9009f06b976 Mon Sep 17 00:00:00 2001
From: thoffman <thoffman@embl.de>
Date: Thu, 16 Jan 2025 17:36:10 +0100
Subject: [PATCH 1/2] adding easyconfigs: HMMER-3.4-gompi-2024a.eb

---
 .../h/HMMER/HMMER-3.4-gompi-2024a.eb          | 63 +++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100644 easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb

diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
new file mode 100644
index 00000000000..f58d56361a1
--- /dev/null
+++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
@@ -0,0 +1,63 @@
+easyblock = 'ConfigureMake'
+
+name = 'HMMER'
+version = '3.4'
+
+homepage = 'http://hmmer.org/'
+description = """HMMER is used for searching sequence databases for homologs
+ of protein sequences, and for making protein sequence alignments. It
+ implements methods using probabilistic models called profile hidden Markov
+ models (profile HMMs).  Compared to BLAST, FASTA, and other sequence
+ alignment and database search tools based on older scoring methodology,
+ HMMER aims to be significantly more accurate and more able to detect remote
+ homologs because of the strength of its underlying mathematical models. In the
+ past, this strength came at significant computational expense, but in the new
+ HMMER3 project, HMMER is now essentially as fast as BLAST."""
+
+toolchain = {'name': 'gompi', 'version': '2024a'}
+
+source_urls = [
+    'http://eddylab.org/software/hmmer/',
+    'http://eddylab.org/software/hmmer%(version_major)s/%(version)s/',
+]
+sources = [SOURCELOWER_TAR_GZ]
+checksums = ['ca70d94fd0cf271bd7063423aabb116d42de533117343a9b27a65c17ff06fbf3']
+
+builddependencies = [
+    ('Python', '3.12.3'),
+    ('Perl', '5.38.2'),
+]
+
+# replace hardcoded /usr/bin/perl shebang lines with '/usr/bin/env perl' across all files
+preconfigopts = "grep '/usr/bin/perl' . | cut -f1 -d: | xargs echo sed -i 's@/usr/bin/perl@/usr/bin/env perl@g' && "
+
+configopts = '--enable-mpi'
+
+buildopts = ' V=1 '
+
+testopts = buildopts
+runtest = 'check'
+
+installopts = ' && cd easel && make install'
+
+local_bin_files = ['alimask', 'esl-afetch', 'esl-alimanip', 'esl-alimap', 'esl-alimask',
+                   'esl-alimerge', 'esl-alipid', 'esl-alirev', 'esl-alistat', 'esl-compalign',
+                   'esl-compstruct', 'esl-construct', 'esl-histplot', 'esl-mask', 'esl-reformat',
+                   'esl-selectn', 'esl-seqrange', 'esl-seqstat', 'esl-sfetch', 'esl-shuffle',
+                   'esl-ssdraw', 'esl-translate', 'esl-weight', 'hmmalign', 'hmmbuild',
+                   'hmmconvert', 'hmmemit', 'hmmfetch', 'hmmlogo', 'hmmpgmd', 'hmmpress',
+                   'hmmscan', 'hmmsearch', 'hmmsim', 'hmmstat', 'jackhmmer', 'makehmmerdb',
+                   'nhmmer', 'nhmmscan', 'phmmer']
+
+sanity_check_paths = {
+    'files': ["bin/%s" % x for x in local_bin_files],
+    'dirs': ['bin', 'share'],
+}
+
+sanity_check_commands = [
+    "esl-construct -h",
+    "hmmsearch -h",
+    "nhmmer -h",
+]
+
+moduleclass = 'bio'

From 5039661bb997482492dfdda54d249928ec4f27ec Mon Sep 17 00:00:00 2001
From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com>
Date: Fri, 17 Jan 2025 13:09:13 +0100
Subject: [PATCH 2/2] Update HMMER-3.4-gompi-2024a.eb

@jpecar Can you please check the header I added?
---
 .../easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
index f58d56361a1..5e40c904940 100644
--- a/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
+++ b/easybuild/easyconfigs/h/HMMER/HMMER-3.4-gompi-2024a.eb
@@ -1,3 +1,19 @@
+##
+# EasyBuild reciPY as per https://github.com/easybuilders/easybuild
+#
+# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA
+# Authors::   Nils Christian <nils.christian@uni.lu>,
+#             Fotis Georgatos <fotis@cern.ch>
+# Updated by: Filip Kružík (INUITS)
+#             Jure Pečar (EMBL)
+# License::   MIT/GPL
+# $Id$
+#
+# This work implements a part of the HPCBIOS project and is a
+#  component of the policy:
+# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html
+##
+
 easyblock = 'ConfigureMake'
 
 name = 'HMMER'